Ogre Battle: MOTBQ captured something that the spinoffs and even the direct sequel never could in my opinion. This is one of my top picks. It unfortunately had a very limited run and is a rare cart so not many got to play it when it was new, and the format unfortunately died off completely. At least, I’ve never seen another attempt at anything quite like it after Ogre Battle 64.
I have to agree with a lot of the RPGs listed here, but did they really get not much love? I guess the Genesis ones were kind of overshadowed by the SNES Squaresoft RPGs of the era. I loved all of these. As for not yet listed here, Breath of Fire 4 is something a lot of people might not know even existed, I never even heard of when it released actually, it wasn’t until nearly a decade later that I got it for PSP, and it was worth it every bit. I’m really sad at what happened to that IP after that point…
For games people have probably never heard of: Mordor: The Depths of Dejenol. Dragon Court 2. The former is a great dungeon crawler where you methodically map out and conquer 15 floors by gradually accumulating better gear and guild levels. It unfortunately uses 16 bit libraries and needs an emulated 32 bit or lower environment to run on a 64 bit modern computer (Win3.1 installed in DosBox, for example) and the license is owned by someone who has sadly made no effort in facilitating this and so it sits, mostly in obscurity, because of the effort barrier required to play. The latter was an online game, where you were given a short blurb and a number of options you could use to get out of any encounter (one which was combat). It had an energy system that was there only to have you explore other options and play multiple characters (they did not sell energy, and there were farmable ingame items that could refresh energy, allowing you to play forever if you were efficient). It is unfortunately now defunct. I spent many an hour on both of them.
I’m not sure how much these flew under the radar at the time, but Master of Orion 2 (NOT 3), and Conquest of the New World: Deluxe Edition as 4x games. Warlords Battlecry 3 as a pseudo RTS (but mostly heavily focused on RPG elements on building your hero). Lords of Magic is a sort of a blend of turn based and real time strategy. Heroes of Might and Magic series - some of them were better than others. I can’t remember exactly which version I preferred, but necropolis was always my favorite faction. Majesty was an excellent spin on the RTS genre where you don’t have direct control over anything (Majesty 2, not so much, avoid that one).
Most of NIS “tactical” RPGs fly under the radar. Disgaea(s), Makai Kingdom, Phantom Brave, La Pucelle: Tactics, Soul Nomad and the World Eaters. They are admittedly niche which is why they don’t get a lot of widespread attention. They focus heavily on a power accumulation cycle as you approach endgame, but in a way that is generally appealing (excluding the parts where you are expected to repeat a specific “grind stage”, which I dislike). If I could try to explain it in simplest terms to someone that has never played one, each game is “breakable” in a different way but the game itself is designed to be broken.
For Tower Defense, the genre in and of itself is pretty niche to begin with. My favorites are Gemcraft: Chasing Shadows, Defenders Quest, and YouTD (a map for Warcraft 3). Gemcraft is a power accumulation tower defense that strays away from straight tower defense mechanics and more into making efficient feedback loops to squeeze the most you can out of a stage as you progress further into “breaking” the game. For fans of a more classic tower defense experience, there is a mode that does not allow you to “break” the game in this manner. Defenders Quest is a tower defense with a bit lighter RPG elements. YouTD, while not technically a “game”, is a crowdsourced tower defense map for Warcraft 3 done as a thesis project and maintained after that (though rarely updated as of now) and is generally excellently balanced (maybe a bit too well).